Use the Rao-Blackwell estimator to get a free energy difference for residues in a CpHMD system.
test.RaoBlackwellEstimator(1) Manual Page
Name
test.RaoBlackwellEstimator - Use the Rao-Blackwell estimator to get a free energy difference for residues in a CpHMD system.
Synopsis
test.RaoBlackwellEstimator [-hV] [--aFi=traj] [--bootstrapIter=100000] [--numSnaps=-1] [--skip=-1] [--sR=<selection>] [--startSnap=-1] [--writeFrequency=100] files…
Description
Options
- --aFi, --arcFile=traj
-
A file containing the the PDB from which to build the ExtendedSystem. There is currently no default.
- --bootstrapIter=100000
-
Number of bootstrap iterations. Set -1 for no bootstrapping.
- -h, --help
-
Print command help and exit.
- --numSnaps=-1
-
Number of snapshots to use from an archive file. Default is all.
- --skip=-1
-
Calculate energies on snaps with this interval.
- --sR, --specifiedResidues=<selection>
-
Specified residues to do analysis.
- --startSnap=-1
-
Start energy evaluations at a snap other than 2.
- -V, --version
-
Print the Force Field X version and exit.
- --writeFrequency=100
-
Calculate the RBE and print at this snapshot read frequency.
Arguments
- files…
-
PDB input file in the same directory as the ARC file.